HPC Crash Course

Fundamentals in Computing & init()

Manuel Holtgrewe

Berlin Institute of Health at Charité

Welcome

  • Course Overview
  • Aims, Scope, Non-Aims, Out-of-Scope

Course Overview

  • Welcome to the course! 👋
  • Introduction to High-Performance Computing (HPC)
  • Focus on biomedical and medical research applications

🔬 ⌨️ 🧬

  • Duration: 5 days 5 x 45 min
  • Instructor: Manuel Holtgrewe
  • Contact Information: manuel.holtgrewe@bih-charite.de

User Engagement

  • We are a large group today.
  • We will use PollEverywhere for
    • quizes for “Lernerfolgskontrolle”
    • questions and answers
  • Let’s try: PollEv.com/manuelholtgrewe153

The Sheep Scale

Course Aims and Scope

  • Basic understanding of HPC
  • Some theory to understand issues occuring in practice
  • How to help yourself in case of troubleshooting
  • Install software (conda, apptainer/singularity)
  • Tips and sleight of hand for improved productivity

… and maybe

  • Connect “birds of a feather” to later share experience, e.g., on project organisation

Course Non-Aims and Out-of-Scope

  • Advanced OnDemand Portal usage
  • (Linux) command line basics
  • Programming basics
  • Scientific programming, e.g., machine learning, statistics, visualization, parameter fitting, polars, …
  • Bioinformatics (variant/gene expression/… analysis)
  • Networking issues with Charite or MDC/MAX
  • Advanced Snakemake usage, reproducibility, …

Course Outline

  1. Fundamentals: Computing
  2. Fundamentals: HPC
  3. Software Installation Management
  4. Slurm Workload Manager
  5. Snakemake for Workflows